# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 06:15:42 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H]1C(=O)n2ncc(C#N)c2N=C1c3cnn(CCN(C)C)c3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 79H  79H  5-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile  ligand  46  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_79H
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 79H  C16  C  CR15  0  -0.058  -1.3023  -1.5768   1.2662
 79H  N3   N  NS    0  -0.245   2.3962   4.5348  -0.6669
 79H  C6   C  CR5   0  -0.319   3.3023   2.1773  -0.2493
 79H  C7   C  CR15  0   0.037   4.6528   1.7316  -0.2572
 79H  N1   N  N     0  -0.253   4.7456   0.4640   0.0235
 79H  N2   N  NR5   0  -0.438   3.4741   0.0514   0.2042
 79H  C8   C  C     0   0.610   3.1278  -1.2507   0.5494
 79H  O    O  O     0  -0.369   3.9565  -2.0715   0.8301
 79H  C3   C  CH1   0  -0.530   1.6457  -1.5105   0.4677
 79H  C1   C  CH1   0  -0.244   1.3177  -2.3170  -0.8392
 79H  C2   C  CH3   0  -0.681   1.8206  -1.6296  -2.1027
 79H  C    C  CH3   0  -0.650   1.8090  -3.7561  -0.7545
 79H  C5   C  CR5   0   0.709   2.5606   1.0561   0.0601
 79H  N    N  N     0  -0.449   1.2322   0.9172   0.2631
 79H  C4   C  C     0   0.274   0.7895  -0.2711   0.5104
 79H  C10  C  CR5   0  -0.209  -0.6090  -0.4396   0.7903
 79H  N6   N  N     0  -0.267  -2.5818  -1.3270   1.4067
 79H  N4   N  NR5   0  -0.270  -2.7427  -0.0520   1.0290
 79H  C11  C  CR15  0   0.099  -1.6032   0.5210   0.6537
 79H  C12  C  CH2   0  -0.297  -4.0706   0.5250   0.9859
 79H  C13  C  CH2   0  -0.274  -4.9093  -0.1113  -0.1195
 79H  N5   N  NT    0  -0.411  -6.1867   0.5562  -0.2531
 79H  C15  C  CH3   0  -0.527  -6.0763   1.8110  -0.9686
 79H  C14  C  CH3   0  -0.520  -7.1743  -0.3024  -0.8741
 79H  H1   H  HCR5  0   0.273  -0.9095  -2.5487   1.5255
 79H  H2   H  HCR5  0   0.304   5.5324   2.3221  -0.4616
 79H  H3   H  HCH1  0   0.335   1.3896  -2.1499   1.3169
 79H  H4   H  HCH1  0   0.274   0.2266  -2.3476  -0.8865
 79H  H5   H  HCH3  0   0.242   1.4700  -0.6007  -2.1948
 79H  H6   H  HCH3  0   0.234   2.9107  -1.6283  -2.1658
 79H  H7   H  HCH3  0   0.259   1.4513  -2.1675  -2.9758
 79H  H8   H  HCH3  0   0.236   1.4539  -4.2494   0.1510
 79H  H9   H  HCH3  0   0.243   1.4272  -4.3150  -1.6096
 79H  H10  H  HCH3  0   0.236   2.8957  -3.8286  -0.7759
 79H  H11  H  HCR5  0   0.312  -1.5548   1.5425   0.3132
 79H  H12  H  HCH2  0   0.276  -4.5457   0.3818   1.9555
 79H  H13  H  HCH2  0   0.263  -3.9430   1.5944   0.8296
 79H  H14  H  HCH2  0   0.210  -4.3347  -0.1115  -1.0609
 79H  H15  H  HCH2  0   0.249  -5.0840  -1.1562   0.1438
 79H  H17  H  HCH3  0   0.198  -5.7318   1.6824  -2.0065
 79H  H18  H  HCH3  0   0.238  -7.0467   2.3077  -0.9986
 79H  H19  H  HCH3  0   0.233  -5.3830   2.4905  -0.4723
 79H  H20  H  HCH3  0   0.236  -7.3116  -1.2085  -0.2832
 79H  H21  H  HCH3  0   0.234  -8.1340   0.2138  -0.9219
 79H  H22  H  HCH3  0   0.195  -6.9072  -0.6037  -1.8986
 79H  C9   C  CSP   0   0.002   2.8015   3.4718  -0.4777

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 79H  C14  N5   single    1.448  0.020  1.448
 79H  C15  N5   single    1.449  0.020  1.449
 79H  N5   C13  single    1.447  0.020  1.447
 79H  C13  C12  single    1.527  0.020  1.527
 79H  C12  N4   single    1.449  0.020  1.449
 79H  N4   C11  aromatic  1.330  0.020  1.330
 79H  N4   N6   aromatic  1.339  0.020  1.339
 79H  C11  C10  aromatic  1.389  0.020  1.389
 79H  N6   C16  aromatic  1.311  0.020  1.311
 79H  N3   C9   triple    1.153  0.020  1.153
 79H  C10  C16  aromatic  1.414  0.020  1.414
 79H  C10  C4   single    1.436  0.020  1.436
 79H  C9   C6   single    1.407  0.020  1.407
 79H  N    C4   double    1.292  0.020  1.292
 79H  N    C5   single    1.351  0.020  1.351
 79H  C    C1   single    1.523  0.020  1.523
 79H  C4   C3   single    1.507  0.020  1.507
 79H  C5   C6   aromatic  1.379  0.020  1.379
 79H  C5   N2   aromatic  1.366  0.020  1.366
 79H  C6   C7   aromatic  1.422  0.020  1.422
 79H  C3   C1   single    1.570  0.020  1.570
 79H  C3   C8   single    1.507  0.020  1.507
 79H  C1   C2   single    1.524  0.020  1.524
 79H  N2   C8   single    1.391  0.020  1.391
 79H  N2   N1   aromatic  1.349  0.020  1.349
 79H  C7   N1   aromatic  1.302  0.020  1.302
 79H  C8   O    double    1.200  0.020  1.200
 79H  C16  H1   single    0.930  0.020  1.080
 79H  C7   H2   single    0.930  0.020  1.080
 79H  C3   H3   single    0.970  0.020  1.090
 79H  C1   H4   single    0.970  0.020  1.090
 79H  C2   H5   single    0.970  0.020  1.090
 79H  C2   H6   single    0.970  0.020  1.090
 79H  C2   H7   single    0.970  0.020  1.090
 79H  C    H8   single    0.970  0.020  1.090
 79H  C    H9   single    0.970  0.020  1.090
 79H  C    H10  single    0.970  0.020  1.090
 79H  C11  H11  single    0.930  0.020  1.080
 79H  C12  H12  single    0.970  0.020  1.090
 79H  C12  H13  single    0.970  0.020  1.090
 79H  C13  H14  single    0.970  0.020  1.090
 79H  C13  H15  single    0.970  0.020  1.090
 79H  C15  H17  single    0.970  0.020  1.090
 79H  C15  H18  single    0.970  0.020  1.090
 79H  C15  H19  single    0.970  0.020  1.090
 79H  C14  H20  single    0.970  0.020  1.090
 79H  C14  H21  single    0.970  0.020  1.090
 79H  C14  H22  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 79H  H1   C16  N6   120.05  3.000
 79H  H1   C16  C10  128.76  3.000
 79H  N6   C16  C10  111.18  3.000
 79H  C5   C6   C7   104.90  3.000
 79H  C7   C6   C9   128.73  3.000
 79H  C5   C6   C9   126.37  3.000
 79H  H2   C7   N1   121.04  3.000
 79H  H2   C7   C6   127.14  3.000
 79H  N1   C7   C6   111.82  3.000
 79H  N2   N1   C7   105.04  3.000
 79H  C5   N2   C8   123.26  3.000
 79H  C8   N2   N1   123.66  3.000
 79H  C5   N2   N1   113.04  3.000
 79H  C3   C8   O    125.04  3.000
 79H  O    C8   N2   121.78  3.000
 79H  C3   C8   N2   113.12  3.000
 79H  H3   C3   C4   109.02  3.000
 79H  H3   C3   C1   107.28  3.000
 79H  C4   C3   C1   109.11  3.000
 79H  H3   C3   C8   106.80  3.000
 79H  C1   C3   C8   109.82  3.000
 79H  C4   C3   C8   114.55  3.000
 79H  H4   C1   C    107.34  3.000
 79H  H4   C1   C2   107.84  3.000
 79H  C    C1   C2   111.46  3.000
 79H  H4   C1   C3   105.01  3.000
 79H  C2   C1   C3   112.92  3.000
 79H  C    C1   C3   111.82  3.000
 79H  H7   C2   H6   107.01  3.000
 79H  H7   C2   H5   106.79  3.000
 79H  H6   C2   H5   108.35  3.000
 79H  H7   C2   C1   109.26  3.000
 79H  H6   C2   C1   112.21  3.000
 79H  H5   C2   C1   112.92  3.000
 79H  H10  C    H9   107.44  3.000
 79H  H10  C    H8   108.12  3.000
 79H  H9   C    H8   107.77  3.000
 79H  H10  C    C1   112.56  3.000
 79H  H9   C    C1   109.13  3.000
 79H  H8   C    C1   111.63  3.000
 79H  N    C5   N2   124.49  3.000
 79H  N2   C5   C6   105.19  3.000
 79H  N    C5   C6   130.24  3.000
 79H  C4   N    C5   117.40  3.000
 79H  C10  C4   N    118.61  3.000
 79H  N    C4   C3   123.81  3.000
 79H  C10  C4   C3   117.53  3.000
 79H  C11  C10  C4   126.63  3.000
 79H  C4   C10  C16  129.59  3.000
 79H  C11  C10  C16  103.78  3.000
 79H  N4   N6   C16  105.56  3.000
 79H  C12  N4   C11  127.27  3.000
 79H  C11  N4   N6   112.76  3.000
 79H  C12  N4   N6   119.85  3.000
 79H  H11  C11  N4   122.43  3.000
 79H  H11  C11  C10  130.86  3.000
 79H  N4   C11  C10  106.71  3.000
 79H  H13  C12  H12  107.95  3.000
 79H  H13  C12  C13  111.72  3.000
 79H  H12  C12  C13  110.50  3.000
 79H  H13  C12  N4   106.75  3.000
 79H  H12  C12  N4   108.73  3.000
 79H  C13  C12  N4   111.05  3.000
 79H  H15  C13  H14  106.81  3.000
 79H  H15  C13  N5   108.81  3.000
 79H  H14  C13  N5   112.40  3.000
 79H  H15  C13  C12  108.19  3.000
 79H  H14  C13  C12  109.39  3.000
 79H  N5   C13  C12  111.07  3.000
 79H  C14  N5   C15  110.71  3.000
 79H  C15  N5   C13  112.19  3.000
 79H  C14  N5   C13  111.59  3.000
 79H  H19  C15  H18  107.13  3.000
 79H  H19  C15  H17  107.63  3.000
 79H  H18  C15  H17  107.80  3.000
 79H  H19  C15  N5   111.31  3.000
 79H  H18  C15  N5   109.89  3.000
 79H  H17  C15  N5   112.85  3.000
 79H  H22  C14  H21  107.59  3.000
 79H  H22  C14  H20  107.90  3.000
 79H  H21  C14  H20  107.83  3.000
 79H  H22  C14  N5   113.32  3.000
 79H  H21  C14  N5   109.76  3.000
 79H  H20  C14  N5   110.24  3.000
 79H  C6   C9   N3   180.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 79H  CONST_01  C11  N4   N6   C16     0.00   0.0  0
 79H  CONST_02  N4   C11  C10  C16     0.00   0.0  0
 79H  CONST_03  N1   N2   C5   C6      0.00   0.0  0
 79H  CONST_04  N2   N1   C7   C6      0.00   0.0  0
 79H  CONST_05  N2   C5   C6   C7      0.00   0.0  0
 79H  CONST_06  C5   N2   N1   C7      0.00   0.0  0
 79H  CONST_07  C5   C6   C7   N1      0.00   0.0  0
 79H  CONST_08  N6   N4   C11  C10     0.00   0.0  0
 79H  CONST_09  N4   N6   C16  C10     0.00   0.0  0
 79H  CONST_10  C11  C10  C16  N6      0.00   0.0  0
 79H  CONST_11  N4   C11  C10  C4    180.00   0.0  0
 79H  CONST_12  N6   C16  C10  C4    180.00   0.0  0
 79H  CONST_13  C12  N4   N6   C16   180.00   0.0  0
 79H  CONST_14  N    C5   C6   C9      0.00   0.0  0
 79H  CONST_15  N2   C5   C6   C9    180.00   0.0  0
 79H  CONST_16  N1   C7   C6   C9    180.00   0.0  0
 79H  CONST_17  C12  N4   C11  C10   180.00   0.0  0
 79H  CONST_18  H11  C11  C10  C16   180.00   0.0  0
 79H  CONST_19  H2   C7   N1   N2    180.00   0.0  0
 79H  CONST_20  H1   C16  C10  C4      0.00   0.0  0
 79H  Var_01    N    C4   C10  C16  -170.23  30.0  2
 79H  Var_02    C3   C8   N2   N1   -170.45  30.0  1
 79H  Var_03    C10  C4   N    C5    177.21  30.0  1
 79H  Var_04    C13  C12  N4   N6    -67.84  30.0  2
 79H  Var_05    N5   C13  C12  N4   -174.17  30.0  2
 79H  Var_06    H8   C    C1   C3     52.31  30.0  3
 79H  Var_07    H5   C2   C1   C3    -53.99  30.0  3
 79H  Var_08    C14  N5   C13  C12  -157.20  30.0  1
 79H  Var_09    H20  C14  N5   C13    59.00  30.0  3
 79H  Var_10    H17  C15  N5   C13    62.83  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 79H  chir_01  C3  C4  C1  C8  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 79H  plan-1  C16  0.020
 79H  plan-1  C4   0.020
 79H  plan-1  C10  0.020
 79H  plan-1  N6   0.020
 79H  plan-1  N4   0.020
 79H  plan-1  C11  0.020
 79H  plan-1  C12  0.020
 79H  plan-1  H1   0.020
 79H  plan-1  H11  0.020
 79H  plan-2  N3   0.020
 79H  plan-2  C6   0.020
 79H  plan-2  C7   0.020
 79H  plan-2  N1   0.020
 79H  plan-2  N2   0.020
 79H  plan-2  C8   0.020
 79H  plan-2  C5   0.020
 79H  plan-2  N    0.020
 79H  plan-2  H2   0.020
 79H  plan-2  C9   0.020
 79H  plan-3  N2   0.020
 79H  plan-3  C8   0.020
 79H  plan-3  O    0.020
 79H  plan-3  C3   0.020

